This application describes a multidisciplinary collaboration between Dr. Michael Sheets, a developmental biologist who focuses on post-transcriptional regulation of early Xenopus embryogenesis and Dr. Colin Dewey, an expert in biostatistics and bioinformatics who focuses on analyzing gene expression using deep sequencing methodologies. While progress has been achieved in understanding Xenopus laevis development from a transcriptional point of view, significantly less is known about the translation of mRNA transcripts into proteins. We propose to use ribosome profiling to globally measure the translational activity of Xenopus mRNAs across the window of development that extends from oogenesis to gastrulation. Results from the proposed experiments will provide an unprecedented view of the dynamic translational landscape that exists during Xenopus development and this data has numerous applications. First, our experiments will identify biologically relevant Xenopus mRNAs. Transcriptome analysis only identifies the mRNAs present in cells, but it cannot define which mRNAs are translated into protein and therefore biologically relevant. We will use ribosome profiling to identify the actively translated and biologically relevant Xenopus mRNAs. This subset of the mRNA population and especially those that exhibit regulation represent ideal candidates for loss of function studies. Second, our results will identify groups of mRNAs that exhibit similar patterns of translational regulation. These co-regulated mRNAs will provide important starting points for molecular studies that seek to identify common sequence motifs for RNA binding proteins or miRNAs that mediate regulation. Third, ribosome profiling in the presence of the inhibitor harringtonine will allow us to identify the translational initiation site(s) for each Xenpus mRNA in our samples. The position of initiation defines the amino termini of the protein product encoded by an mRNA and therefore globally identifying the initiation sites of all mRNAs defines the N-terminus of the proteome. In addition, identifying the sites of initiation for specific mRNAs can reveal the presence of 5'RNA sequences, called uORFs that often function to regulate translational initiation. Results from the proposed experiments will provide an unprecedented genomic scale analysis of mRNA translation in Xenopus and how the translation of each mRNA changes during development. Our results and the associated methods will be useful for Xenopus researchers and researchers addressing the same questions in other vertebrate embryos.

Public Health Relevance

Proteins are the molecular machines that perform the functions of all living cells. Our research is focused on how proteins are synthesized and how this synthesis changes depending upon the individual needs of specific cells.

National Institute of Health (NIH)
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Exploratory/Developmental Grants (R21)
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Special Emphasis Panel (ZRG1-GGG-A (50))
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Coulombe, James N
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University of Wisconsin Madison
Schools of Medicine
United States
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